SAXSdb — 7zs4

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Cytochrome c

Methylococcus capsulatus str. Bath

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 1 HEME C × 2 DI(HYDROXYETHYL)ETHER × 2 GLYCEROL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	G1UBD5_METCA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–158； UniProt 1–158 Author chain B； PDBConstruct 1–158； UniProt 1–158

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	7zs4
Deposition date deposition_date	2022-05-06
Structure title title	F32V Cytochrome c prime beta from Methylococcus capsulatus (Bath)
Keywords keywords	Cytochrome c prime, Beta-sheet, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

7zs4__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

7zs4__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7zs4__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	20.37 Å
Rg (electron density)	19.36 Å
Total Rg	20.23 Å
Atom count	2206
Residues	272
Excluded volume	38766 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7zs4__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Cytochrome c
Molecular weight formula_weight	17322.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2379

MNKPSFLLVGLLVVSGVLGAAETKVKYPDGFRSWYHVKSMVIQPGHPLENPVGGIHHVYANAEAIQGLRGGNYPDGAVLVFDLFDYQEDNHALVEGKRKLIGVMERDAKRFSATGGWGYEGFGEGKPDKRLVTDGGQGCFGCHAAQKESQYVFSRLRD

Source Source

Source organism organism	Methylococcus capsulatus str. Bath
NCBI taxonomy ID ncbi_taxonomy_id	243233
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	HEME C
Molecular weight formula_weight	618.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	138

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Unit-cell length a length_a	105.674 Å
Unit-cell length b length_b	105.674 Å
Unit-cell length c length_c	105.674 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	P 21 3
Space-group number int_tables_number	198
Crystal system crystal_system	—

Resolution resolution	1.750 Å
Low-resolution limit resolution_low	74.710 Å
R factor r_factor	0.1875
R_work r_work	0.1862
R_free r_free	0.2131

F32V Cytochrome c prime beta from Methylococcus capsulatus (Bath)

1. Protein Identity and Related Structures Protein Identity & Related Structures

Cytochrome c

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7zs4__assembly_1__model_1

7zs4__assembly_1__model_1 | I(q)

7zs4__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (1)

F32V Cytochrome c prime beta from Methylococcus capsulatus (Bath)

1. Protein Identity and Related Structures Protein Identity & Related Structures

Cytochrome c

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7zs4__assembly_1__model_1

7zs4__assembly_1__model_1 | I(q)

7zs4__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (1)